crossing96/oncoscreening huggingface dataset:
A radiogenomics signature for predicting the clinical outcome of bladder urothelial carcinoma.	OBJECTIVES: To determine the integrative value of contrast-enhanced computed tomography (CECT), transcriptomics data and clinicopathological data for predicting the survival of bladder urothelial carcinoma (BLCA) patients. METHODS: RNA sequencing data, radiomics features and clinical parameters of 62 BLCA patients were included in the study. Then, prognostic signatures based on radiomics features and gene expression profile were constructed by using least absolute shrinkage and selection operator (LASSO) Cox analysis. A multi-omics nomogram was developed by integrating radiomics, transcriptomics and clinicopathological data. More importantly, radiomics risk score-related genes were identified via weighted correlation network analysis and submitted to functional enrichment analysis. RESULTS: The radiomics and transcriptomics signatures significantly stratified BLCA patients into high- and low-risk groups in terms of the progression-free interval (PFI). The two risk models remained independent prognostic factors in multivariate analyses after adjusting for clinical parameters. A nomogram was developed and showed an excellent predictive ability for the PFI in BLCA patients. Functional enrichment analysis suggested that the radiomics signature we developed could reflect the angiogenesis status of BLCA patients. CONCLUSIONS: The integrative nomogram incorporated CECT radiomics, transcriptomics and clinical features improved the PFI prediction in BLCA patients and is a feasible and practical reference for oncological precision medicine. KEY POINTS: • Our radiomics and transcriptomics models are proved robust for survival prediction in bladder urothelial carcinoma patients. • A multi-omics nomogram model which integrates radiomics, transcriptomics and clinical features for prediction of progression-free interval in bladder urothelial carcinoma is established. • Molecular functional enrichment analysis is used to reveal the potential molecular function of radiomics signature.	bladder
Adaptation to Extreme Environments in an Admixed Human Population from the Atacama Desert.	Inorganic arsenic (As) is a toxic xenobiotic and carcinogen associated with severe health conditions. The urban population from the Atacama Desert in northern Chile was exposed to extremely high As levels (up to 600 µg/l) in drinking water between 1958 and 1971, leading to increased incidence of urinary bladder cancer (BC), skin cancer, kidney cancer, and coronary thrombosis decades later. Besides, the Andean Native-American ancestors of the Atacama population were previously exposed for millennia to elevated As levels in water (∼120 µg/l) for at least 5,000 years, suggesting adaptation to this selective pressure. Here, we performed two genome-wide selection tests-PBSn1 and an ancestry-enrichment test-in an admixed population from Atacama, to identify adaptation signatures to As exposure acquired before and after admixture with Europeans, respectively. The top second variant selected by PBSn1 was associated with LCE4A-C1orf68, a gene that may be involved in the immune barrier of the epithelium during BC. We performed association tests between the top PBSn1 hits and BC occurrence in our population. The strongest association (P = 0.012) was achieved by the LCE4A-C1orf68 variant. The ancestry-enrichment test detected highly significant signals (P = 1.3 × 10-9) mapping MAK16, a gene with important roles in ribosome biogenesis during the G1 phase of the cell cycle. Our results contribute to a better understanding of the genetic factors involved in adaptation to the pathophysiological consequences of As exposure.	bladder
Usefulness of droplet digital PCR and Sanger sequencing for detection of FGFR3 mutation in bladder cancer.	OBJECTIVE: The purpose of our research was to determine the usefulness of different methods for detecting Y373C mutation of gene FGFR3. PATIENTS AND METHODS TOTAL: 138 primary bladder cancer patients (71cases G1 and 67 cases G2-G3) were included in the study. Tumor tissue and urine samples were collected and kept frozen until the isolation of DNA. Sanger sequencing was applied for detecting mutation in cancer and ddPCR was utilized for urine assessment. RESULTS: ddPCR appears to be more effective and it identified FGFR3 mutation (Y373C) in urinary sediment in 20.3% of cases whereas Sanger sequencing did in 15.5%. Only in 8/39 (20.5%) cases the mutation was observed both in urine and tissue. In 12/39 (30.8%) cases (5G1 and 7 G2-G3) we did not detect any FGFR3 mutation in urine although it was confirmed by sequencing. We only found mutation in urine in 20/39 cases (15 G1, 5 G2-G3) (51.3%). The correlation between the presence of FGFR3 mutations and better survival was confirmed. The Log-Rank test indicates a significant difference in the likelihood of survival for patients with the FGFR3 mutation but without recurrence (Cox's F-test P = 0.17006; Log-Rank Test P = 0.00059). CONCLUSION: ddPCR appeared to be more sensitive method for detection FGFR3 gene mutation particularly for detecting low levels of tumor DNA amongst a large excess of nontumor DNA. It is significant as the implementation of such markers into routine practice could be beneficial. The prospective study in larger cohort is needed.	bladder
The impact of age on intravesical instillation of Bacille Calmette-Guerin treatment in patients with high-grade T1 bladder cancer.	Intravesical instillation of Bacille Calmette-Guèrin (BCG) is the standard adjuvant treatment for high-risk non muscle invasive bladder cancer (NMIBC). Since its mechanism of action is supposed to be linked to the immune system efficiency and senescence could negatively affect this efficiency, BCG efficacy in the elderly has been questioned. This study aimed to assess the impact of age on BCG efficacy and safety in patients with high-grade T1 bladder cancer (BC).Among 123 patients with high-grade T1 BCG scheduled for BCG treatment, 82 were <75 year-old (group A) and 41 were ≥75 year-old (group B). Follow-up: urine cytology and cystoscopy every 3 months for the first 2 years, every 6 months for the third year, and then yearly. Tumor recurrence was defined as pathological evidence of disease at the bladder biopsy; tumor progression was defined as pathological shift to muscle invasive disease at the bladder biopsy or the imaging techniques showing recurrent BC and distant metastasis likely related to it.The median follow-up was 65 months (range 11-152). Recurrence occurred in 35 patients, 19 (23.2%) in the group A and 16 (39%) in the group B. Progression occurred in 18 patients, 12 (14.6%) in the group A and 6 (14.6%) in the group B. Recurrence free rate was similar in both groups up to 2 years. The 5 years progression rate was almost the same in both groups A and B (85.9% vs 84.7%), whereas the 5 years cancer-specific survival (CSS) was 92.6% in the group A and 85.4% in the group B. Of the 18 patients with progression, 11 underwent cystectomy; 12 patients died because of their BC. Kaplan-Meier plots pointed out no difference in recurrence-free, progression-free, and CSS between the 2 groups. Adverse events were similar in the 2 groups. Only 4 (3.3%) patients, 2 (2.4%) in the group A and 2 (4.8%) in the group B, experienced mild adverse reactions compatible with treatment.Elderly patients with high-grade T1 BC are not poorer candidates to BCG treatment, as they had similar benefit and adverse reactions than those aging ≥75 years.	bladder
Possible correlation of sonic hedgehog signaling with epithelial-mesenchymal transition in muscle-invasive bladder cancer progression.	PURPOSE: To investigate the role of sonic hedgehog (Shh) signaling and epithelial-mesenchymal transition (EMT) in bladder cancer progression and invasion. METHODS: We cultured three bladder cancer cell lines, muscle-invasive T24 and 5637, and non-muscle-invasive KK47, in the presence of a recombinant-Shh (r-Shh) protein or cyclopamine, a Shh signaling inhibitor, to investigate proliferation and expression of EMT markers. Wound-healing assays and transwell assay were performed to evaluate cell invasion and migration. Mice were then inoculated with bladder cancer cells and treated with cyclopamine. Mouse tumor samples were stained for Shh signaling and EMT markers. RESULTS: R-Shh protein enhanced cell proliferation, whereas cyclopamine significantly suppressed cell proliferation, especially in invasive cancer (5637 and T24) (p < 0.05). R-Shh protein promoted EMT, suppressed E-cadherin and enhanced N-cadherin and vimentin and Gli1, an Shh downstream molecule, while cyclopamine blocked EMT, especially in 5637 and T24. Cyclopamine also inhibited cell invasion and migration in vitro. In the animal study, intraperitoneal injection of cyclopamine significantly suppressed tumor growth in 5637 and T24 in mice (p = 0.01 and p = 0.004, respectively) and slightly suppressing KK47 tumor growth (p = 0.298). Significant cyclopamine-induced suppression of Gli1 in 5637 and T24 mouse tumors (both p = 0.03) was seen, suggesting that muscle-invasive bladder cancer may be more dependent on Shh signaling than non-muscle-invasive bladder cancer. CONCLUSIONS: Shh signaling and EMT were especially enhanced in muscle-invasive bladder cancer progression and invasion, and suppressed by the inhibition of Shh signaling.	bladder
Predictive Factors for Residual Cancer in Second Transurethral Resection for Non-muscle-invasive Bladder Cancer.	BACKGROUND/AIM: The significance of second transurethral resection (TUR), and identification of predictive factors for residual cancer remain unrevealed. This study aimed to find residual cancer and up-staging rates, as well as predictive factors for residual cancer, in patients who undergo second TUR for non-muscle-invasive bladder cancer (NMIBC). PATIENTS AND METHODS: Patients who underwent second TURs for NMIBC between 2015 and 2017, were included in the study and their clinicopathological characteristics were analyzed for predictors of residual cancer. RESULTS: Among 143 Japanese patients whose tumors were initially diagnosed as high-risk NMIBC, residual cancers detected at second TURs were, Tis: n=22 (15.4%), Ta: n=15 (10.5%) and T1: n=29 (20.3%). No patients showed up-staging from NMIBC to MIBC. The presence of carcinoma-in situ at initial TUR was an independent risk factor for any residual cancer (Tis, Ta and T1), non-flat residual cancer (Ta and T1), and flat residual cancer (Tis). CONCLUSION: The presence of carcinoma-in situ is suggested to be an independent predictor of residual cancer. This may help guide decisions to perform second TUR.	bladder
PRIMARY MALIGNANT MELANOMA OF THE URINARY BLADDER: CASE REPORT.	Primary malignant melanoma of the urinary bladder is rare, with only 20 cases reported to date. We present a case of an 87-year-old woman with multiple comorbidities who presented with advanced urinary bladder neoplasm. Histopathologic analysis suggested melanoma of the urinary bladder. No previous or concurrent diagnosis of cutaneous melanoma was documented. The patient underwent transurethral resection of the tumor before and during hospitalization at our hospital but died shortly after due to widespread disease. Autopsy was not performed.	bladder
Fatty acid oxidation inhibitor etomoxir suppresses tumor progression and induces cell cycle arrest via PPARγ-mediated pathway in bladder cancer.	Tumor cells rely on aerobic glycolysis as their main energy resource (Warburg effect). Recent research has highlighted the importance of lipid metabolism in tumor progression, and certain cancers even turn to fatty acids as the main fuel. Related studies have identified alterations of fatty acid metabolism in human bladder cancer (BCa). Our microarray analysis showed that fatty acid metabolism was activated in BCa compared with normal bladder. The free fatty acid (FFA) level was also increased in BCa compared with paracancerous tissues. Inhibition of fatty acid oxidation (FAO) with etomoxir caused lipid accumulation, decreased adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH) levels, suppressed BCa cell growth in vitro and in vivo, and reduced motility of BCa cells via affecting epithelial-mesenchymal transition (EMT)-related proteins. Furthermore, etomoxir induced BCa cell cycle arrest at G(0)/G(1) phase through peroxisome proliferator-activated receptor (PPAR) γ-mediated pathway with alterations in fatty acid metabolism associated gene expression. The cell cycle arrest could be reversed by PPARγ antagonist GW9662. Taken together, our results suggest that inhibition of FAO with etomoxir may provide a novel avenue to investigate new therapeutic approaches to human BCa.	bladder
Morphologic and genomic characterization of urothelial to sarcomatoid transition in muscle-invasive bladder cancer.	INTRODUCTION: The sarcomatoid morphology of muscle-invasive bladder cancer (MIBC) is associated with unfavorable prognosis. However, the genomic, transcriptomic, and proteomic relationship between conventional urothelial and synchronous sarcomatoid morphology is poorly defined. METHODS: We compiled a cohort of 21 MIBC patients with components of conventional urothelial and adjacent sarcomatoid morphology within the same tumor focus. We performed comprehensive pathologic and immunohistochemical characterization and in 4 selected cases, subjected both morphologic components to targeted DNA sequencing and whole transcriptome analysis. RESULTS: Synchronous sarcomatoid and urothelial morphology from the same MIBC foci shared truncal somatic mutations, indicating a common ancestral clone. However, additional mutations or copy number alterations restricted to the either component suggested divergent evolution at the genomic level. This was confirmed at the transcriptome level since while the urothelial component exhibited a basal-like subtype (TCGA2014: cluster III, LundTax: basal/squamous-like), the sarcomatoid morphology was predominantly cluster IV (claudin-low). Protein expression was consistent with a basal-like phenotype in both morphologies in 18/21 of cases. However, most cases had evidence of active epithelial-to-mesenchymal transition (E-Cad ↓ and Zeb1 or TWIST1 ↑) from urothelial toward the sarcomatoid morphology. Drug response signatures nominated different targets for each morphology and proposed agents under clinical investigation in liposarcoma or other sarcoma. PD-L1 expression was higher in the sarcomatoid than the urothelial component. CONCLUSIONS: Conventional urothelial and adjacent sarcomatoid morphologies of MIBC arise from the same common ancestor and share a basal-like phenotype. However, divergence between the morphologies at the genome, transcriptome, and proteome level suggests differential sensitivity to therapy.	bladder
Comparative effectiveness of palliative chemotherapy versus neoadjuvant chemotherapy followed by radical cystectomy versus cystectomy followed by adjuvant chemotherapy versus cystectomy for regional node-positive bladder cancer: A retrospective analysis: KCSG GU 17-03.	The regional lymph node-positive bladder cancer was classified as stage IV in the AJCC 7th edition but was changed to stage IIIB in the 8th edition, revised in 2018. Among the various studies involving immune checkpoint inhibitors, groups that had only lymph node metastasis showed better outcomes than those with distant metastasis. Therefore, it is necessary to rethink the treatment strategy for lymph node-positive bladder cancer. The aim of this study was to compare the treatment outcomes of chemotherapy, surgery, and combination therapy in patients with lymph node-positive bladder cancer. From 1 January 2010 to 31 December 2015, patients with bladder cancer presenting local lymph node metastasis at the time of diagnosis were treated with a single treatment strategy, with either radical cystectomy or chemotherapy or with a combined strategy using both. Treatment outcomes were retrospectively analyzed on the basis of clinical indices and survival time. Out of 230 patients with bladder cancer, 44 (19.1%) were treated with palliative chemotherapy, 30 (13.0%) with neoadjuvant chemotherapy followed by cystectomy, 129 (56.1%) with cystectomy followed by adjuvant chemotherapy, and 27 (11.7%) with cystectomy alone. Median survival among all groups was 30.4 months. For each group, median overall survival was 19.3, 49.1, 42.6, and 11.2 months, respectively. This study represents an advancement in understanding the impact of clinical treatment patterns of lymph node-positive bladder cancer through comparison of survival data of patients treated with different therapeutic strategies. Combined treatment resulted in better outcomes than did single treatments.	bladder
Distinct genetic alterations and luminal molecular subtype in nested variant of urothelial carcinoma.	AIMS: Nested variant of urothelial carcinoma (NVUC) is rare, and only a few small series exist. Molecular characteristics and the classifying marker profile as well as therapeutic targets of this specific variant are mostly unknown. The aim of this study was to characterise NVUC at the molecular level in one of the largest cohorts to date. In addition, we applied an immunohistochemical marker panel in order to define the molecular subtype. METHODS AND RESULTS: Sixty NVUC cases were collected from different departments. TERT promoter mutation analysis was carried out in all samples using SNaPshot analysis. Targeted sequencing of 48 cancer-related genes by next-generation sequencing (NGS) analysis was performed in a subset of 26 cases. Immunohistochemical markers CD44, CK5, CK14, EGFR, p63, FOXA1, GATA3, CD24 and CK20 were used to elucidate the molecular subtype. A total of 62.5% of NVUC cases harboured a mutation of the TERT promoter. Additionally, TP53, JAK3 and CTNNB1 were among the most frequently mutated genes identified by NGS analysis. Subtyping revealed that all NVUC express luminal markers such as CD24, FOXA1, GATA3 and CK20. CONCLUSIONS: In summary, NVUC belong to the luminal molecular subtype. Moreover, a subset of NVUC seems to be characterised by mutations of the Wnt and inflammatory pathways, including JAK3 mutations, indicating a different biological background compared to conventional urothelial bladder cancer.	bladder
Label-free grading and staging of urothelial carcinoma through multimodal fibre-probe spectroscopy.	Urothelial carcinoma (UC) is the most common bladder tumour. Proper treatment requires tumour resection for diagnosing its grade (aggressiveness) and stage (invasiveness). White-light cystoscopy and histopathological examination are the gold standard procedures for clinical and histopathological diagnostics, respectively. However, cystoscopy is limited in terms of specificity, histology requires long tissue processing, both procedures rely on operator's experience. Multimodal optical spectroscopy can provide a powerful tool for detecting, staging and grading bladder tumours in a fast, reliable and label-free modality. In this study, we collected fluorescence, Raman and reflectance spectra from 50 biopsies obtained from 32 patients undergoing transurethral resection of bladder tumour using a multimodal fibre-probe. Principal component analysis allowed distinguishing normal from pathological tissues, as well as discriminating tumour stages and grades. Each individual spectroscopic technique provided high specificity and sensitivity in classifying all tissues; however, a multimodal approach resulted in a considerable increase in diagnostic accuracy (≥95%), which is of paramount importance for tumour grading and staging. The presented method offers the potential for being applied in cystoscopy and for providing an automated diagnosis of UC at the clinical level, with an improvement with respect to current state-of-the-art procedures.	bladder
NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype.	The epithelial-mesenchymal transition (EMT) is a key process implicated in cancer metastasis and therapy resistance. Recent studies have emphasized that cells can undergo partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype - a cornerstone of tumour aggressiveness and poor prognosis. These cells can have enhanced tumour-initiation potential as compared to purely epithelial or mesenchymal ones and can integrate the properties of cell-cell adhesion and motility that facilitates collective cell migration leading to clusters of circulating tumour cells (CTCs) - the prevalent mode of metastasis. Thus, identifying the molecular players that can enable cells to maintain a hybrid E/M phenotype is crucial to curb the metastatic load. Using an integrated computational-experimental approach, we show that the transcription factor NRF2 can prevent a complete EMT and instead stabilize a hybrid E/M phenotype. Knockdown of NRF2 in hybrid E/M non-small cell lung cancer cells H1975 and bladder cancer cells RT4 destabilized a hybrid E/M phenotype and compromised the ability to collectively migrate to close a wound in vitro. Notably, while NRF2 knockout simultaneously downregulated E-cadherin and ZEB-1, overexpression of NRF2 enriched for a hybrid E/M phenotype by simultaneously upregulating both E-cadherin and ZEB-1 in individual RT4 cells. Further, we predict that NRF2 is maximally expressed in hybrid E/M phenotype(s) and demonstrate that this biphasic dynamic arises from the interconnections among NRF2 and the EMT regulatory circuit. Finally, clinical records from multiple datasets suggest a correlation between a hybrid E/M phenotype, high levels of NRF2 and its targets and poor survival, further strengthening the emerging notion that hybrid E/M phenotype(s) may occupy the 'metastatic sweet spot'.	bladder
Impact of model misspecification in shared frailty survival models.	Survival models incorporating random effects to account for unmeasured heterogeneity are being increasingly used in biostatistical and applied research. Specifically, unmeasured covariates whose lack of inclusion in the model would lead to biased, inefficient results are commonly modeled by including a subject-specific (or cluster-specific) frailty term that follows a given distribution (eg, gamma or lognormal). Despite that, in the context of parametric frailty models, little is known about the impact of misspecifying the baseline hazard or the frailty distribution or both. Therefore, our aim is to quantify the impact of such misspecification in a wide variety of clinically plausible scenarios via Monte Carlo simulation, using open-source software readily available to applied researchers. We generate clustered survival data assuming various baseline hazard functions, including mixture distributions with turning points, and assess the impact of sample size, variance of the frailty, baseline hazard function, and frailty distribution. Models compared include standard parametric distributions and more flexible spline-based approaches; we also included semiparametric Cox models. The resulting bias can be clinically relevant. In conclusion, we highlight the importance of fitting models that are flexible enough and the importance of assessing model fit. We illustrate our conclusions with two applications using data on diabetic retinopathy and bladder cancer. Our results show the importance of assessing model fit with respect to the baseline hazard function and the distribution of the frailty: misspecifying the former leads to biased relative and absolute risk estimates, whereas misspecifying the latter affects absolute risk estimates and measures of heterogeneity.	bladder